Enhancement of CPU/juicer.sh in error judgement of genomePath

[xuzhougeng]

Describe the bug

In https://github.com/aidenlab/juicer/blob/master/CPU/juicer.sh, it use if [ -z "$genomePath" ] to judge whether the genomePath is set or not , but even you set the unexisted file to -z, it will not stop.

For example, use -z

genomePath=test
[ -z "$genomePath" ] && echo file existed || echo file not existed 

it will return file existed, but if you use -f

[ -f "$genomePath" ] && echo file existed || echo file not existed

it will return file not existed, which will be more robust .

so, it may be better to use -d for directory related parameter and -f for file related parameter.

[nchernia]

Thanks, we will look into it or feel free to resolve and send a pull request.

On Sat, Aug 24, 2019 at 12:41 AM xuzhougeng [email protected] wrote:

Describe the bug

In https://github.com/aidenlab/juicer/blob/master/CPU/juicer.sh, it use if [ -z "$genomePath" ] to judge whether the genomePath is set or not , but even you set the un-existed file to -z.

For example

genomePath=test [ -z "$genomePath" ] && echo file existed || echo file not existed

it will return file existed, but

[ -f "$genomePath" ] && echo file existed || echo file not existed

it will return file not existed, which will be more robust .

so, it may be better to use -d for directory related parameter and -f for file related parameter.

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